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- EMDB-66509: Cryo-EM structure of the flagellar filament in Vibrio parahaemoly... -

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Basic information

Entry
Database: EMDB / ID: EMD-66509
TitleCryo-EM structure of the flagellar filament in Vibrio parahaemolyticus VP288
Map data
Sample
  • Complex: Cryo-EM structure of the flagellar filament in Vibrio parahaemolyticus VP288
    • Protein or peptide: Flagellin
KeywordsFlagella / Vibrio parahaemolyticus / Filament / FlaA / Locomotion / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesVibrio parahaemolyticus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsNg CH
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)T11-104/22-R Hong Kong
CitationJournal: To Be Published
Title: High resolution structures of flagella from Vibrio Cholerae and Vibrio parahaemolyticus: Insights into the basis of swimming and swarming
Authors: Liu XB / Zhang YY / Ng CH / Wang ZL / Leung KP / Li SR / Zheng SQ / Heng H / Cheng QP / Xu YT / Chen KC / Xie MM / Sun RY / Luo M / Lau CY / Chen S
History
DepositionOct 9, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66509.png

Downloads & links

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Map

FileDownload / File: emd_66509.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 228 pix.
= 241.68 Å		1.06 Å/pix.
x 228 pix.
= 241.68 Å		1.06 Å/pix.
x 228 pix.
= 241.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-0.33286166 - 0.8343172
Average (Standard dev.)0.027006162 (±0.10039557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions228228228
Spacing228228228
CellA=B=C: 241.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_66509_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66509_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66509_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the flagellar filament in Vibrio parahaemoly...

EntireName: Cryo-EM structure of the flagellar filament in Vibrio parahaemolyticus VP288
Components
  • Complex: Cryo-EM structure of the flagellar filament in Vibrio parahaemolyticus VP288
    • Protein or peptide: Flagellin

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Supramolecule #1: Cryo-EM structure of the flagellar filament in Vibrio parahaemoly...

SupramoleculeName: Cryo-EM structure of the flagellar filament in Vibrio parahaemolyticus VP288
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio parahaemolyticus (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO
Source (natural)Organism: Vibrio parahaemolyticus (bacteria)
Molecular weightTheoretical: 39.886809 KDa
SequenceString: MAINVNTNVS AMTAQRYLNH AAEGQQKSME RLSSGYKINS AKDDAAGLQI SNRLNAQSRG LDMAVKNAND GISIAQVAEG AMNESTNIL QRMRDLSLQS ANGSNSKAER VAIQEEVTAL NDELNRIAET TSFGGNKLLN GTYGTQSFQI GADSGEAVML S MGSLRSDT ...String:
MAINVNTNVS AMTAQRYLNH AAEGQQKSME RLSSGYKINS AKDDAAGLQI SNRLNAQSRG LDMAVKNAND GISIAQVAEG AMNESTNIL QRMRDLSLQS ANGSNSKAER VAIQEEVTAL NDELNRIAET TSFGGNKLLN GTYGTQSFQI GADSGEAVML S MGSLRSDT SAMGGKSYSA EEGKDASWTV GDKTELKMSY TNKQGEEKEL TIKAKQGDDI EQLATYINGQ SEDVKASVGE DG KLQVFAS TQKVNGEVEF SGNLAGEIGF GDAKDVTVKD IDVTTVAGSQ EAVAVIDGAL KSVDSQRASL GAFQNRFNHA ISN LDNINE NVNASNSRIK DTDYAKETTA MTKSQILQQA STSILAQAKQ SPSAALSLLG

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
50.0 mMNaClSodium Chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.73 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 56802
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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